[ccp4bb] Suggestions for Initial crystal screening

Hi all, I have purified a protein, the gel filtration and Native-PAGE shows it is very homogeneous. There is no problem when I concentrated it to 20mg/mL. However, I found above 85% conditions will cause protein precipitation when I try to crystallize it even at 2mg/mL. I also tried to add

Re: [ccp4bb] Composit omit map vs. ligand

In addition to excellent Kay's reply.. Also make sure to check refined B factors. Note, if the ligand is not there then that volume is likely filled with bulk-solvent. Now low occupancy in combination with very large B factors may approximate bulk-solvent quite well. The Polder map along with

Re: [ccp4bb] Parallelization?

I think Intel has it in the parallel studio. BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dyda Sent: Thursday, February 9, 2017 1:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Parallelization? Am I correct that OpenMP parallelized

Re: [ccp4bb] Parallelization?

Am I correct that OpenMP parallelized crystallographic software is in Fortran? While I think there is OpenMP extensions for C and variants, but not so for python. Is this correct? Fred *** Fred Dyda, Ph.D.

Re: [ccp4bb] Parallelization?

Dear Bernhard, After Kay showed me how to do it by making SHELXL parallel, I was able to make SHELXD, ANODE and SHELXT (my current small molecule direct methods program) highly parallel. I'm still working on SHELXE because it requires major changes. In principle chain tracing is difficult to

Re: [ccp4bb] Parallelization?

Hi Bernhard, I parallelized ESSENS, SHELXL, CNS and a few other programs, and wrote a paper about it (long time ago, in J. Appl. Cryst I think). It's actually not difficult to parallelize with OpenMP, but it needs time - developers seemingly rather spend their time on other things. Automatic

[ccp4bb] Parallelization?

Hi Developers, I am wondering whether we fully utilize our hardware, and knowing not much about the finer detail, I'd like to ask a few questions. Most workstations have 6-12 or more cores, and equipped with plenty of cheap memory and SSD arrays and some overclocking, these machines are

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A joint project between the SBGrid Consortium at Harvard Medical School and the Dataverse Team at the Institute for Quantitative Social Science at Harvard University has an immediate opening for a developer to help us build a next generation data publication system for large biomedical datasets.

[ccp4bb] The paper describing wwPDB OneDep system is now available.

The paper describing wwPDB OneDep system is now available. The wwPDB has deployed a unified system for deposition, biocuration, and validation of macromolecular structures globally across all wwPDB,

Re: [ccp4bb] AW: [ccp4bb] Problem with MolRep

Check solvent % - as suggested low solvent content means tight packing means poor signal. Check matthews coefficient ? Do you expect several molecules? As suggested - does the model form an oligamer? ( You need to be careful with these - sometimes you generate thm using both crystal and

Re: [ccp4bb] Composit omit map vs. ligand

Dear colleagues, First of all, I would like to thank to all who responded! I have selected some answers and my reactions to sum up: 1) Kay Diedrichs - try a Polder map: clear density for the ligand at 3 sigma appeared. 2) JR Helliwell - build first five atoms and check the density now (read

[ccp4bb] AW: [ccp4bb] Problem with MolRep

Dear Madhurima, Small protein structures can be very difficult to solve by MR due to an unfavorable ratio between inter- and intra-molecular vectors in the pattersons. I am currently also struggling with some data sets myself. However, there are things you could (and should) try: 1) If